Solvent Accessibility Mapping of HBV ε RNA

To assess the solvent accessibility in HBV $\text{ε}$ , ¹H-¹³C HSQC spectra were collected in the absence and presence of MRI contrast dye gadolinium-diethylenetriamine pentaacetic acid-bismethylamide (Gd-DTPA-BMA) from (OmniScan—GE Healthcare) (Hartlmüller al., 2017 (link)). All measurements were collected with uniformly ¹³C/¹⁵N-labeled 500 µM HBV $\text{ε}$ RNA in buffer A on a Bruker 800 MHz triple resonance cryoprobe. Using a saturation-recovery approach, proton longitudinal (R₁) relaxation rates were measured as a function of increasing dye concentration (0.8 to 4.2 mM). The slope of the best fit linear relationship between dye concentration and proton R₁ gave the sPRE value for each measured proton. Errors in sPRE measurements were determined by propagating the standard deviations of repeated delay points in R₁ experiments.